Strain identifier
BacDive ID: 2728
Type strain: 
Species: Acetivibrio thermocellus
Strain Designation: LQ8
Strain history: <- J. G. Zeikus, Universityof Wisconsin, Departments of Biochemistry and Agricultural Bacteriology, Madison, USA; LQ8 <- L. Y. Quinn
NCBI tax ID(s): 637887 (strain), 1515 (species)
version 8.1 (current version)
General
@ref: 511
BacDive-ID: 2728
DSM-Number: 1313
keywords: genome sequence, Bacteria, anaerobe, spore-forming, thermophilic, Gram-positive, alcohol production
description: Acetivibrio thermocellus LQ8 is an anaerobe, spore-forming, thermophilic bacterium that produces alcohol.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 637887 | strain |
| 1515 | species |
strain history
- @ref: 511
- history: <- J. G. Zeikus, Universityof Wisconsin, Departments of Biochemistry and Agricultural Bacteriology, Madison, USA; LQ8 <- L. Y. Quinn
doi: 10.13145/bacdive2728.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Eubacteriales
- family: Oscillospiraceae
- genus: Acetivibrio
- species: Acetivibrio thermocellus
- full scientific name: Acetivibrio thermocellus (Viljoen et al. 1926) Tindall 2019
synonyms
@ref synonym 20215 Ruminiclostridium thermocellum 20215 Clostridium thermocellum 20215 Hungateiclostridium thermocellum
@ref: 511
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Oscillospiraceae
genus: Acetivibrio
species: Acetivibrio thermocellus
full scientific name: Acetivibrio thermocellus (Viljoen et al. 1926) Tindall 2019
strain designation: LQ8
type strain: no
Morphology
cell morphology
- @ref: 69480
- gram stain: positive
- confidence: 100
Culture and growth conditions
culture medium
- @ref: 511
- name: ACETIVIBRIO MEDIUM (DSMZ Medium 122)
- growth: yes
- link: https://mediadive.dsmz.de/medium/122
- composition: Name: ACETIVIBRIO MEDIUM (DSMZ Medium 122) Composition: Cellulose 10.0 g/l (optional) Na2-ß-glycerophosphate x 5 H2O 6.0 g/l K2HPO4 5.5 g/l Cellobiose 5.0 g/l Yeast extract 4.5 g/l MgCl2 x 6 H2O 2.6 g/l KH2PO4 1.43 g/l (NH4)2SO4 1.3 g/l L-Glutathione 0.25 g/l CaCl2 x 2 H2O 0.13 g/l FeSO4 x 7 H2O 0.0011 g/l Sodium resazurin 0.0005 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range | confidence |
|---|---|---|---|---|---|
| 511 | positive | growth | 60 | thermophilic | |
| 69480 | thermophilic | 99.999 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 511 | anaerobe | |
| 69480 | anaerobe | 100 |
spore formation
- @ref: 69480
- spore formation: yes
- confidence: 99.998
compound production
- @ref: 511
- compound: ethanol
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 43410 | 62968 | cellulose | + | degradation |
| 43410 | 17057 | cellobiose | + | degradation |
| 43410 | 17234 | glucose | + | growth |
Isolation, sampling and environmental information
isolation
- @ref: 511
- geographic location: Iowa
- country: USA
- origin.country: USA
- continent: North America
Safety information
risk assessment
- @ref: 511
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Acetivibrio thermocellus DSM 1313 | GCA_000184925 | complete | ncbi | 637887 |
| 66792 | Clostridium thermocellum DSM 1313 | 637887.3 | complete | patric | 637887 |
| 66792 | Hungateiclostridium thermocellum strain DSM 1313 | 1515.11 | wgs | patric | 1515 |
| 66792 | Hungateiclostridium thermocellum LQ8, DSM 1313 | 650377924 | complete | img | 637887 |
| 66792 | Acetivibrio thermocellus DSM 1313 | 2825454334 | draft | img | 1515 |
GC content
- @ref: 511
- GC-content: 39.5
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 66 | no |
| motile | yes | 51.884 | no |
| flagellated | no | 70.969 | no |
| gram-positive | yes | 52.059 | no |
| anaerobic | yes | 99.999 | yes |
| aerobic | no | 99.111 | yes |
| halophile | no | 94.272 | no |
| spore-forming | yes | 94.781 | no |
| glucose-util | yes | 84.249 | no |
| thermophile | yes | 99.681 | yes |
| glucose-ferment | yes | 57.683 | no |
External links
@ref: 511
culture collection no.: DSM 1313
straininfo link
- @ref: 72256
- straininfo: 1975
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Pathogenicity | 14766568 | Electrotransformation of Clostridium thermocellum. | Tyurin MV, Desai SG, Lynd LR | Appl Environ Microbiol | 10.1128/AEM.70.2.883-890.2004 | 2004 | Anti-Bacterial Agents/pharmacology, Clostridium/drug effects/*genetics/growth & development, DNA Primers, Drug Resistance, Bacterial/genetics, Electroporation/*instrumentation/*methods, Erythromycin/pharmacology, Escherichia coli/drug effects/genetics/growth & development, Gene Transfer Techniques, Isoniazid/pharmacology, Lincomycin/pharmacology, *Transformation, Bacterial | |
| Stress | 16332787 | Role of spontaneous current oscillations during high-efficiency electrotransformation of thermophilic anaerobes. | Tyurin MV, Sullivan CR, Lynd LR | Appl Environ Microbiol | 10.1128/AEM.71.12.8069-8076.2005 | 2005 | Bacteria, Anaerobic/*physiology, Clostridium thermocellum/*physiology, Electricity, Electrophysiology, Escherichia coli/physiology, Hot Temperature, Oscillometry, Thermoanaerobacterium/*physiology | |
| Genetics | 21460082 | Complete genome sequence of the cellulolytic thermophile Clostridium thermocellum DSM1313. | Feinberg L, Foden J, Barrett T, Davenport KW, Bruce D, Detter C, Tapia R, Han C, Lapidus A, Lucas S, Cheng JF, Pitluck S, Woyke T, Ivanova N, Mikhailova N, Land M, Hauser L, Argyros DA, Goodwin L, Hogsett D, Caiazza N | J Bacteriol | 10.1128/JB.00322-11 | 2011 | Anaerobiosis, Cellulose/metabolism, Clostridium thermocellum/*genetics/metabolism/physiology, DNA, Bacterial/*chemistry/*genetics, *Genome, Bacterial, Hot Temperature, Molecular Sequence Data, *Sequence Analysis, DNA | Metabolism |
| 22559230 | Dcm methylation is detrimental to plasmid transformation in Clostridium thermocellum. | Guss AM, Olson DG, Caiazza NC, Lynd LR | Biotechnol Biofuels | 10.1186/1754-6834-5-30 | 2012 | |||
| Metabolism | 23645383 | Characterization of Clostridium thermocellum strains with disrupted fermentation end-product pathways. | van der Veen D, Lo J, Brown SD, Johnson CM, Tschaplinski TJ, Martin M, Engle NL, van den Berg RA, Argyros AD, Caiazza NC, Guss AM, Lynd LR | J Ind Microbiol Biotechnol | 10.1007/s10295-013-1275-5 | 2013 | Acetic Acid/metabolism, Amino Acids/metabolism, Bacteria, Anaerobic/genetics/growth & development/metabolism, Biomass, Cellobiose/metabolism, Clostridium thermocellum/genetics/growth & development/*metabolism, Ethanol/metabolism, *Fermentation, Lactic Acid/metabolism | |
| Enzymology | 26373940 | Expression and characterization of a new thermostable esterase from Clostridium thermocellum. | Zhang T, Chen H, Ni Z, Tian R, Jia J, Chen Z, Yang S | Appl Biochem Biotechnol | 10.1007/s12010-015-1824-7 | 2015 | Amino Acid Sequence, Cloning, Molecular, Clostridium thermocellum/*enzymology/*genetics, Enzyme Stability, Esterases/*chemistry/*genetics/isolation & purification/metabolism, Gene Expression, Hydrogen-Ion Concentration, Metals/pharmacology, Molecular Sequence Data, *Temperature | Genetics |
| 26692898 | Clostridium thermocellum DSM 1313 transcriptional responses to redox perturbation. | Sander K, Wilson CM, Rodriguez M Jr, Klingeman DM, Rydzak T, Davison BH, Brown SD | Biotechnol Biofuels | 10.1186/s13068-015-0394-9 | 2015 | |||
| Metabolism | 27213504 | Genetic engineering of Clostridium thermocellum DSM1313 for enhanced ethanol production. | Kannuchamy S, Mukund N, Saleena LM | BMC Biotechnol | 10.1186/s12896-016-0260-2 | 2016 | Alcohol Dehydrogenase/*genetics/metabolism, Bioreactors/microbiology, Clostridium thermocellum/classification/*physiology, Ethanol/isolation & purification/*metabolism, Genetic Enhancement/*methods, Metabolic Engineering/methods, Pyruvate Carboxylase/*genetics/metabolism, Recombinant Proteins/genetics/metabolism, Species Specificity, Zymomonas/*physiology | Phylogeny |
| Phenotype | 27602057 | Exploring complex cellular phenotypes and model-guided strain design with a novel genome-scale metabolic model of Clostridium thermocellum DSM 1313 implementing an adjustable cellulosome. | Thompson RA, Dahal S, Garcia S, Nookaew I, Trinh CT | Biotechnol Biofuels | 10.1186/s13068-016-0607-x | 2016 | ||
| Metabolism | 28003194 | LacI Transcriptional Regulatory Networks in Clostridium thermocellum DSM1313. | Wilson CM, Klingeman DM, Schlachter C, Syed MH, Wu CW, Guss AM, Brown SD | Appl Environ Microbiol | 10.1128/AEM.02751-16 | 2017 | Bacterial Proteins/chemistry/genetics, Cellobiose/metabolism, Cellulose/metabolism, Clostridium thermocellum/*enzymology/*genetics/growth & development, Disaccharides/metabolism, Fermentation, Gene Expression Regulation, Bacterial/*genetics, *Gene Regulatory Networks, Genome, Bacterial, Glycoside Hydrolases/drug effects/genetics, Lipoproteins/antagonists & inhibitors/*genetics/*metabolism, Operon/genetics, Panicum/metabolism, Polysaccharides/genetics, Regulon/*genetics, Sequence Analysis, RNA, Sequence Deletion, Transcription Factors, Transcriptome, Up-Regulation | Transcriptome |
| Biotechnology | 28344648 | Cellulosic ethanol production via consolidated bioprocessing by a novel thermophilic anaerobic bacterium isolated from a Himalayan hot spring. | Singh N, Mathur AS, Tuli DK, Gupta RP, Barrow CJ, Puri M | Biotechnol Biofuels | 10.1186/s13068-017-0756-6 | 2017 | ||
| 28409424 | Enhanced saccharification of lignocellulosic agricultural biomass and increased bioethanol titre using acclimated Clostridium thermocellum DSM1313. | Nisha M, Saranyah K, Shankar M, Saleena LM | 3 Biotech | 10.1007/s13205-017-0606-z | 2017 | |||
| Metabolism | 28671264 | Overflow metabolism and growth cessation in Clostridium thermocellum DSM1313 during high cellulose loading fermentations. | Thompson RA, Trinh CT | Biotechnol Bioeng | 10.1002/bit.26374 | 2017 | Cell Proliferation/*physiology, Cellulose/*metabolism, Clostridium thermocellum/classification/*physiology, Computer Simulation, Energy Metabolism/*physiology, Fermentation, Hydrogen/metabolism, Metabolic Flux Analysis/*methods, Metabolic Networks and Pathways/*physiology, *Models, Biological, Species Specificity | Phylogeny |
| 28932263 | How does cellulosome composition influence deconstruction of lignocellulosic substrates in Clostridium (Ruminiclostridium) thermocellum DSM 1313? | Yoav S, Barak Y, Shamshoum M, Borovok I, Lamed R, Dassa B, Hadar Y, Morag E, Bayer EA | Biotechnol Biofuels | 10.1186/s13068-017-0909-7 | 2017 | |||
| 29344087 | Determination of the native features of the exoglucanase Cel48S from Clostridium thermocellum. | Liu YJ, Liu S, Dong S, Li R, Feng Y, Cui Q | Biotechnol Biofuels | 10.1186/s13068-017-1009-4 | 2018 | |||
| Metabolism | 29537062 | Engineering cellulolytic bacterium Clostridium thermocellum to co-ferment cellulose- and hemicellulose-derived sugars simultaneously. | Xiong W, Reyes LH, Michener WE, Maness PC, Chou KJ | Biotechnol Bioeng | 10.1002/bit.26590 | 2018 | Aldose-Ketose Isomerases/genetics/metabolism, Anaerobiosis, Cellobiose/metabolism, Cellulose/*metabolism, Cloning, Molecular, Clostridium thermocellum/*genetics/growth & development/*metabolism, *Fermentation, Glucose/metabolism, Metabolic Engineering/*methods, Phosphotransferases (Alcohol Group Acceptor), Polysaccharides/*metabolism, Recombinant Proteins/genetics/metabolism, Thermoanaerobacter/enzymology/genetics, Xylose/metabolism | Enzymology |
| 29632556 | Clostridium thermocellum LL1210 pH homeostasis mechanisms informed by transcriptomics and metabolomics. | Whitham JM, Moon JW, Rodriguez M Jr, Engle NL, Klingeman DM, Rydzak T, Abel MM, Tschaplinski TJ, Guss AM, Brown SD | Biotechnol Biofuels | 10.1186/s13068-018-1095-y | 2018 | |||
| 30377946 | Resonance assignments of a cellulosomal double-dockerin from Clostridium thermocellum. | Chen C, Yang H, Xuan J, Cui Q, Feng Y | Biomol NMR Assign | 10.1007/s12104-018-9859-7 | 2018 | Bacterial Proteins/*chemistry, Cellulosomes/*chemistry, Clostridium thermocellum/*chemistry, Nitrogen Isotopes, *Nuclear Magnetic Resonance, Biomolecular, Protein Structure, Secondary, Protons | ||
| Genetics | 31406903 | Draft genome sequence data of Clostridium thermocellum PAL5 possessing high cellulose-degradation ability. | Nakazono-Nagaoka E, Fujikawa T, Shikata A, Tachaapaikoon C, Waeonukul R, Pason P, Ratanakhanokchai K, Kosugi A | Data Brief | 10.1016/j.dib.2019.104274 | 2019 | Metabolism | |
| 31802632 | CRISPR interference (CRISPRi) as transcriptional repression tool for Hungateiclostridium thermocellum DSM 1313. | Ganguly J, Martin-Pascual M, van Kranenburg R | Microb Biotechnol | 10.1111/1751-7915.13516 | 2019 | *Clustered Regularly Interspaced Short Palindromic Repeats, Gene Expression, Metabolic Networks and Pathways, *RNA, Guide | ||
| Metabolism | 33051021 | Construction of lactic acid overproducing Clostridium thermocellum through enhancement of lactate dehydrogenase expression. | Mazzoli R, Olson DG, Lynd LR | Enzyme Microb Technol | 10.1016/j.enzmictec.2020.109645 | 2020 | Acetates/metabolism, Clostridium thermocellum/genetics/growth & development/*metabolism, Ethanol/metabolism, Fermentation, Gene Expression, Genome, Bacterial/genetics, L-Lactate Dehydrogenase/*genetics/metabolism, Lactic Acid/*biosynthesis, Metabolic Engineering, Promoter Regions, Genetic | Enzymology |
| 33876380 | NMR chemical shift assignments of a module of unknown function in the cellulosomal secondary scaffoldin ScaF from Clostridium thermocellum. | Li J, Chen C, Liu YJ, Cui Q, Bayer EA, Feng Y | Biomol NMR Assign | 10.1007/s12104-021-10025-8 | 2021 | *Clostridium thermocellum | ||
| Biotechnology | 33971924 | Identification and characterization of proteins of unknown function (PUFs) in Clostridium thermocellum DSM 1313 strains as potential genetic engineering targets. | Poudel S, Cope AL, O'Dell KB, Guss AM, Seo H, Trinh CT, Hettich RL | Biotechnol Biofuels | 10.1186/s13068-021-01964-4 | 2021 | ||
| Biotechnology | 35227303 | Composition and yield of non-cellulosic and cellulosic sugars in soluble and particulate fractions during consolidated bioprocessing of poplar biomass by Clostridium thermocellum. | Biswal AK, Hengge NN, Black IM, Atmodjo MA, Mohanty SS, Ryno D, Himmel ME, Azadi P, Bomble YJ, Mohnen D | Biotechnol Biofuels Bioprod | 10.1186/s13068-022-02119-9 | 2022 |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 511 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1313) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-1313 | |||
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
| 43410 | Shahar Yoav, Yoav Barak, Melina Shamshoum, Ilya Borovok, Raphael Lamed, Bareket Dassa, Yitzhak Hadar, Ely Morag and Edward A. Baye | 10.1186/s13068-017-0909-7 | How does cellulosome composition influence deconstruction of lignocellulosic substrates in Clostridium (Ruminiclostridium) thermocellum DSM 1313? | Biotechnol Biofuels 10: - 2017 | 28932263 | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 72256 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID1975.1 | StrainInfo: A central database for resolving microbial strain identifiers |